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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build…
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
- Alexander D. MacKerell, D. Bashford, M. Karplus
- ChemistryThe journal of physical chemistry. B
- 14 April 1998
The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
CHARMM: The biomolecular simulation program
An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Evaluation of comparative protein modeling by MODELLER
- A. Sali, Liz Potterton, F. Yuan, H. V. van Vlijmen, M. Karplus
- Biology, ChemistryProteins
- 1 November 1995
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for…
Effective energy function for proteins in solution
Results reported elsewhere show that EEF1 clearly distinguishes correctly from incorrectly folded proteins, both in static energy evaluations and in molecular dynamics simulations and that unfolding pathways obtained by high‐temperature Molecular dynamics simulations agree with those obtained by explicit water simulations.
Crystallographic R Factor Refinement by Molecular Dynamics
Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced and the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.
Molecular dynamics simulations of biomolecules
A brief description of the origin and early uses of biomolecular simulations is presented, some recent studies that illustrate the utility of such simulations are outlined and their ever-increasing potential for contributing to biology is discussed.
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
The pKa values are very sensitive to the details of the local protein conformation, and it is likely that side-chain mobility has an important role in determining the observed pKa shifts.
CHARMM: The Energy Function and Its Parameterization
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.
- B. Brooks, M. Karplus
- Physics, ChemistryProceedings of the National Academy of Sciences…
- 1 November 1983
The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.